In Mist She Was Standing - The climax. 'IN MIST, ENROBED THE TWIIILIIIIIIIIIIIGHT she was standing....' The way that scream reverberates over the whisper is amazing... and then the acoustic guitar comes in. @_@
The Twilight Is My Robe - After he quietly sings, 'Unto you I whisper the wildest dreams,' then it comes in heavy and he screams a line, then just screams when that new melody comes in... man. If you listen closely, his voice kind of breaks at the very end of the scream and his normal voice comes through very, very briefly. That's what makes it so awesome, to me.
The Night and the Silent Water - The second half of the song. Beautiful, soft acoustic guitars, and then the build up to the climax....
Black Rose Immortal - 'Lullaby of the crescent moon took you' until '... black rose immortal...'
April Ethereal - 'She, laughing and weeping at once: "Take me away...."' The 'take me away' is executed perfectly.
The Amen Corner - 'Eerie circles upon the waters... RAHHHHHHHHH!!' That part's awesome.
Karma - The a capella harmony that Mikael sings when the song makes its first big transition, and then the scream following it. That part is overwhelming. Then the beautiful riff before and during the 'The cold season drift over the land' section. And then, of course, that final scream.
Epilogue - The tapped part of the solo, and then the final melody. Just weakeningly beautiful.
Godhead's Lament - The solo towards the beginning of the song that introduces the 'Searching my way to perplexion' melody. Perfect solo.
Serenity Painted Death - 'Darkness reared its head.' Need I say more?
Bleak - The way the song rises back up after the 'Help me cure you' section, and the drifting lead guitar (e-bow) in the background.
Blackwater Park - The way it swells back up after the soft section, and, as everyone has mentioned already, 'Lepers coiled 'neath the trees.' Holy cow.
Wreath - 'End of a search, coming of morning.' Beautiful acoustic break.
Windowpane - The second solo!! Holy crap! @_@
The Baying of the Hounds - Towards the end, when they're playing an almost happy sounding riff, and he growls that wicked, 'Ooooohhh.'
Isolation Years - The whole song. Man. Just perfect. Just heartbreaking.